rmelting

R Interface to MELTING 5

https://github.com/aravind-j/rmelting

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R Interface to MELTING 5

README.Rmd

---
output: rmarkdown::github_document
---

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "",
  fig.path = "inst/extdata/"
)
```

## `rmelting`: R Interface to MELTING 5 

```{r,echo = FALSE, message = FALSE}
devtools::load_all(".")

```

###### Version : [`r getNamespaceVersion("rmelting")`](https://aravind-j.github.io/rmelting/); License: [GPL-2|GPL-3](https://www.r-project.org/Licenses/)

##### *Aravind, J.^1^ and Krishna, G. K.^2^*

1. Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi
2. Division of Crop Physiology, ICAR-Indian Agricultural Research Institute, New Delhi

***

[![minimal R version](https://img.shields.io/badge/R>%3D-3.6-6666ff.svg)](https://cran.r-project.org/)
[![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
```{r, results='asis', echo=FALSE}
dver <- ifelse(test = as.numeric(gsub("(.\\.)(\\d+)(\\..)", "\\2", getNamespaceVersion("rmelting"))) %% 2 != 0, yes = getNamespaceVersion("rmelting"), no = gsub("Version:\\s*", "", readLines(paste0("https://raw.githubusercontent.com/", "aravind-j/rmelting", "/master/DESCRIPTION"))[grep("Version:", readLines(paste0("https://raw.githubusercontent.com/", "aravind-j/rmelting", "/master/DESCRIPTION")))]))

cat(paste("[![develVersion](https://shields.io/badge/devel%20version-", dver, "-orange?logo=github&style=flat)](https://github.com/aravind-j/rmelting)", sep = ""))
```
[![Github Code Size](https://img.shields.io/github/languages/code-size/aravind-j/rmelting.svg)](https://github.com/aravind-j/rmelting)
[![R-CMD-check-bioc](https://github.com/aravind-j/rmelting/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/aravind-j/rmelting/actions/workflows/check-bioc.yml)
[![Project Status: WIP](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![lifecycle](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-yellowgreen.svg)](/commits/master)
[![Website - pkgdown](https://img.shields.io/website-up-down-green-red/https/aravind-j.github.io/rmelting.svg)](https://aravind-j.github.io/rmelting/)
[![.](https://pro-pulsar-193905.appspot.com/UA-116683292-1/welcome-page)](https://github.com/aravind-j/google-analytics-beacon)

***









## Description
`r gsub("\\n", " ", packageDescription("rmelting", fields = "Description"))`

## Installation
The package can be installed from Bioconductor as follows.

```{r, eval=FALSE}
if (!"BiocManager" %in% rownames(installed.packages())) 
  install.packages("BiocManager")
BiocManager::install("rmelting")
```

The development version can be installed from github as follows.

```{r, eval=FALSE}
if (!require('devtools')) install.packages('devtools')
devtools::install_github("aravind-j/rmelting")
```

## Detailed tutorial
For a detailed tutorial on how to used this package type:

```{r, eval=FALSE}
browseVignettes(package = 'rmelting')
```

## What's new
To know whats new in this version type:

```{r, eval=FALSE}
news(package='rmelting')
```

## Links

[Bioconductor page](https://doi.org/doi:10.18129/B9.bioc.rmelting)

[Github page](https://github.com/aravind-j/rmelting)

[Documentation website](https://aravind-j.github.io/rmelting/)



## Bioconductor checks and metrics

```{r, results='asis', echo=FALSE, warning=FALSE}


pkg <- "rmelting"

pkgr <- "missing"
pkgd <- "missing"

page <- httr::GET("https://www.bioconductor.org/install/")
page <- httr::content(page, as = 'text', encoding = "UTF-8")

bcr <- sub('.*(
The current release of Bioconductor is version\n.*?;).*', '\\1', page)
bcd <- sub('.*(
The development version of Bioconductor is version\n.*?;).*', '\\1', page)

bcr <- gsub(".*\n(.+);$", "\\1", bcr)
bcd <- gsub(".*\n(.+);$", "\\1", bcd)

rpr <- as.data.frame(available.packages(repos = paste("https://bioconductor.org/packages/",
                                                      bcr, "/bioc", sep = "")))
rpd <- as.data.frame(available.packages(repos = paste("https://bioconductor.org/packages/",
                                                      bcd, "/bioc", sep = "")))
pkgr <- rpr[rpr$Package == "rmelting", ]$Version
pkgd <- rpd[rpd$Package == "rmelting", ]$Version

colr <- ifelse(pkgr == "missing", "lightgrey", "brightgreen")
cold <- ifelse(pkgd == "missing", "lightgrey", "orange")

bcr_badge <- paste0("https://img.shields.io/badge/",
                    "Bioconductor%20release", "-", bcr, "-", colr, ".svg")

bcd_badge <- paste0("https://img.shields.io/badge/",
                    "Bioconductor%20devel", "-", bcd, "-", cold, ".svg")

pkgr_badge <- paste0("https://img.shields.io/badge/",
                     "BioC%20release", "-", pkgr, "-", colr, ".svg")

pkgd_badge <- paste0("https://img.shields.io/badge/",
                     "BioC%20devel", "-", pkgd, "-", cold, ".svg")

badgedf1 <- rbind(c(name = "Bioc release version",
                    svg = bcr_badge,
                    link = "https://bioconductor.org/install/"),
                  c(name = "Pkg Bioc release version",
                    svg = pkgr_badge,
                    link = "https://bioconductor.org/packages/release/bioc/html/rmelting.html"),
                  c(name = "in Bioc release",
                    svg = "https://bioconductor.org/shields/years-in-bioc/rmelting.svg",
                    link = "https://bioconductor.org/packages/release/bioc/html/rmelting.html#since"),
                  c(name = "Bioc release status",
                    svg = "https://bioconductor.org/shields/build/release/bioc/rmelting.svg",
                    link = "http://bioconductor.org/checkResults/release/bioc-LATEST/rmelting/"),
                  c(name = "Bioc Download rank",
                    svg = "https://bioconductor.org/shields/downloads/release/rmelting.svg",
                    link = "http://bioconductor.org/packages/stats/bioc/rmelting/"))
badgedf2 <- rbind(c(name = "Bioc devel version",
                    svg = bcd_badge,
                    link = "https://bioconductor.org/install/"),
                  c(name = "Pkg Bioc devel version",
                    svg = pkgd_badge,
                    link = "https://bioconductor.org/packages/devel/bioc/html/rmelting.html"),
                  c(name = "in Bioc devel",
                    svg = "https://bioconductor.org/shields/years-in-bioc/rmelting.svg",
                    link = "https://bioconductor.org/packages/devel/bioc/html/rmelting.html#since"),
                  c(name = "Bioc devel status",
                    svg = "https://bioconductor.org/shields/build/devel/bioc/rmelting.svg",
                    link = "http://bioconductor.org/checkResults/devel/bioc-LATEST/rmelting/"),
                  c(name = "Bioc Download rank",
                    svg = "https://bioconductor.org/shields/downloads/devel/rmelting.svg",
                    link = "http://bioconductor.org/packages/stats/bioc/rmelting/"))


badgedf1 <- as.data.frame(badgedf1)
badgedf2 <- as.data.frame(badgedf2)

badgedf <- rbind(paste("[![", badgedf1$name, "](", badgedf1$svg, ")](", badgedf1$link, ")"),
                 paste("[![", badgedf2$name, "](", badgedf2$svg, ")](", badgedf2$link, ")"))


knitr::kable(badgedf, col.names = NULL, format = "html")
```

## Citing `rmelting`
To cite the methods in the package use:

```{r, eval = FALSE}
citation("rmelting")
```

```{r, echo = FALSE}
detach("package:rmelting", unload=TRUE)
suppressPackageStartupMessages(library(rmelting))
cit <- citation("rmelting")
# yr <- format(Sys.Date(), "%Y")
# cit[1]$year <- yr
# oc <- class(cit)
# 
# cit <- unclass(cit)
# attr(cit[[1]],"textVersion") <- gsub("\\(\\)",
#                                      paste("\\(", yr, "\\)", sep = ""),
#                                      attr(cit[[1]],"textVersion"))
# class(cit) <- oc
cit
```

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